Just a guess that this is the back end...
When I open a news group with 0.9.7, a few of the messages are duplicated, show
up at the head of the list, in a weird threading mode (looks like they are
threaded).
Clicking on the thread icon a couple of times sorts things out.
I'll attach a screen shot.

Created attachment 63158[details]
Snapshot showing duplicated messages
The top six messages are the duplicated ones. At least four of them are, and
I've opened the threads containing those articles so they are easy to see.
I run the reader in unread (and threaded of course) mode.
Interestingly, when I click on the messages that appear to be properly
threaded, they appear, but the message line doesn't come "un-bolded" so they
still look like they are unread. (The green flag doesn't clear either).

I still see this with 0.9.8-latest (2002012605 for linux).
My settings are Threaded mode, show Unread messages. Have you tried those
settings to reproduce this?
Also, you might want to use a news server that's not very fast. It seems looking
at how things come up that these messages show up in the wrong place after
rendering of the tree has begun, but messages are still being inserted.

The behavior of this seems to have changed with 0.9.9. Now it looks like the
messages that aren't threaded are not duplicate messages, but unique ones.
Changing to OS All since duplicate was from Windows

This may have been a duplicate of bug 111895 - I saw this behaviour while
working on that bug. This bug was that the threading was incorrect when you
first selected the group - thread children would not appear under their thread
header. However, if you then attempted to open the thread header, the child
then also showed up in its correct threaded spot - hence you had the dupe - the
original in the incorrect spot, then in the correct spot when the thread was
expanded.

Mark,
It looks like your fix landed 9 days prior to 0.9.9 (what I'm using). Was it not
approved for that release?
If not, I will grab a nightly or build from the tip and see if things are better
now and (if they are) close out the bug.
Please advise.